Combining methods for non-invasive fecal DNA enables whole genome and metagenomic analyses in wildlife biology

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Non-invasive biological samples benefit studies that investigate rare, elusive, endangered, or dangerous species. Integrating genomic techniques that use non-invasive biological sampling with advances in computational approaches can benefit and inform wildlife conservation and management. Here, we used non-invasive fecal DNA samples to generate low- to medium-coverage genomes (e.g., >90% of the complete nuclear genome at six X-fold coverage) and metagenomic sequences, combining widely available and accessible DNA collection cards with commonly used DNA extraction and library building approaches. DNA preservation cards are easy to transport and can be stored non-refrigerated, avoiding cumbersome or costly sample methods. The genomic library construction and shotgun sequencing approach did not require enrichment or targeted DNA amplification. The utility and potential of the data generated was demonstrated through genome scale and metagenomic analyses of zoo and free-ranging African savanna elephants (Loxodonta africana). Fecal samples collected from free-ranging individuals contained an average of 12.41% (5.54–21.65%) endogenous elephant DNA. Clustering of these elephants with others from the same geographic region was demonstrated by a principal component analysis of genetic variation using nuclear genome-wide SNPs. Metagenomic analyses identified taxa that included Loxodonta, green plants, fungi, arthropods, bacteria, viruses and archaea, showcasing the utility of this approach for addressing complementary questions based on host-associated DNA, e.g., pathogen and parasite identification. The molecular and bioinformatic analyses presented here contributes towards the expansion and application of genomic techniques to conservation science and practice.
OriginalsprogEngelsk
Artikelnummer1021004
TidsskriftFrontiers in Genetics
Vol/bind13
Antal sider14
ISSN1664-8021
DOI
StatusUdgivet - 2023

Bibliografisk note

Funding Information:
For funding, we thank the International Fund for Animal Welfare; the Conservation Ecology Research Unit (CERU) of the University of Pretoria; and the US Fish and Wildlife Service African Elephant Conservation Fund, grant F22AP01215-00. Alida de Flamingh was supported by funding from the University of Illinois at Urbana-Champaign. Patrícia Pečnerová received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 892446. For samples from free-ranging elephants, we thank CERU. For samples from elephants in zoos, we thank Lara Metrione and Linda Penfold of the South-East Zoo Alliance for Reproduction and Conservation; Dianna Lydick, Lora Baumhardt and the Dallas Zoo; and Fatima Ramis, Corey Neatrou and the Jacksonville Zoo and Gardens. Collection and export/import of elephant dung was sanctioned by appropriate authorities prior to collection, including South African National Parks, the Department of Agriculture, Forestry and Fisheries in South Africa and the United States Department of Agriculture in the United States of America.

Funding Information:
For funding, we thank the International Fund for Animal Welfare; the Conservation Ecology Research Unit (CERU) of the University of Pretoria; and the US Fish and Wildlife Service African Elephant Conservation Fund, grant F22AP01215-00. Alida de Flamingh was supported by funding from the University of Illinois at Urbana-Champaign. Patrícia Pečnerová received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 892446. For samples from free-ranging elephants, we thank CERU. For samples from elephants in zoos, we thank Lara Metrione and Linda Penfold of the South-East Zoo Alliance for Reproduction and Conservation; Dianna Lydick, Lora Baumhardt and the Dallas Zoo; and Fatima Ramis, Corey Neatrou and the Jacksonville Zoo and Gardens. Collection and export/import of elephant dung was sanctioned by appropriate authorities prior to collection, including South African National Parks, the Department of Agriculture, Forestry and Fisheries in South Africa and the United States Department of Agriculture in the United States of America.

Publisher Copyright:
Copyright © 2023 de Flamingh, Ishida, Pečnerová, Vilchis, Siegismund, van Aarde, Malhi and Roca.

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